Effectiveness of DNA Barcoding Primers in Red Algae (Rhodophyta) Identification

Authors

  • Aidil Zaid Khan Agrotechnology Study Program, Faculty of Agriculture, Universitas Padjadjaran, Sumedang
  • Ardian Putra Fernando Department of Biology, Faculty of Mathematics and Natural Sciences, IPB University, Bogor 16680, Indonesia
  • Edo Agam Pamungkas Production Technology of Crop Plantation Study Program, Politeknik Kelapa Sawit Citra Widya Edukasi, Bekasi 17520, Indonesia
  • Ayu Andhira Forestry Engineering Study Program, Faculty of Forestry, Universitas Hasanuddin, Makassar 90245, Indonesia
  • Rifa Nur Ishlah Southeast Asian Regional Centre for Tropical Biology (SEAMEO BIOTROP), Bogor 16134, Indonesia
  • Denia Dwi Citra Resmi Southeast Asian Regional Centre for Tropical Biology (SEAMEO BIOTROP), Bogor 16134, Indonesia
  • Farida Damayanti Department of Agronomy, Faculty of Agriculture, Universitas Padjadjaran, Sumedang 45363, Indonesia
  • Dewi Rahmawati Southeast Asian Regional Centre for Tropical Biology (SEAMEO BIOTROP), Bogor 16134, Indonesia

Keywords:

DNA barcoding, genetic identification, primer, seaweed

Abstract

Red algae (Rhodophyta) are vital primary producers in marine ecosystems and are economically significant due to their wide use in food, pharmaceutical, and cosmetic industries. The significant utilization of red algae indicates that these organisms require conservation and protection from extinction, therefore, accurate identification is a must. Traditional morphological approaches face challenges due to their simplicity and plasticity; however, molecular techniques, such as DNA barcoding can overcome these limitations. This study evaluated the effectiveness of using ITS1, Cox2-3, rbcL 1, and rbcL 2 primers for barcoding seven red algae species, focusing on amplification success and sequencing quality. All of the above-mentioned primers have demonstrated a noteworthy amplification rate of success, with 100% efficacy observed for ITS1 and rbcL 2. However, only Cox2-3, rbcL 1, and rbcL 2 primers exhibited a high-quality read based on the sequencing quality score, indicating their reliability in capturing the target sequence for identification. The results strongly suggested that rbcL 2 is the optimal choice for identifying Rhodophyta due to its high amplification rate and high-quality sequencing results.

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Published

2025-03-18

How to Cite

Khan, A. Z., Fernando, A. P., Pamungkas, E. A., Andhira, A., Ishlah, R. N., Resmi, D. D. C., … Rahmawati, D. (2025). Effectiveness of DNA Barcoding Primers in Red Algae (Rhodophyta) Identification. BIODIVERS - BIOTROP Science Magazine, 4(1), 1–8. Retrieved from https://journal.biotrop.org/index.php/biodivers/article/view/2491

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Vol. 4 No. 1 (2025): Vol. 4 No. 1 (2025): BIODIVERS Volume 4 No. 1 (2025)

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Copyright (c) 2025 Aidil Zaid Khan, Ardian Putra Fernando, Edo Agam Pamungkas, Ayu Andhira, Rifa Nur Ishlah, Denia Dwi Citra Resmi, Farida Damayanti, Dewi Rahmawati

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